Revision as of 14:20, 4 July 2014

• ImageJ's Google+ page
• Fiji's Google+ page
• ImageJ 1.x documentation
• ImageJ User Manual
• Fluorescence image analysis introduction
• ImageJ Documentation Wiki
• About the relationship between ImageJ2 and Fiji
• Wikipedia page on ImageJ
• Wikipedia page on Fiji
• Fiji on OHLOH
• ObjectJ

Links to the contributors' personal pages can be found here.

More ImageJ plugins

• Plugins on the ImageJ website, specifically links to external websites
• Plugins on the ImageJ Documentation Wiki
• The Biomedical Imaging Group in Lausanne has many interesting plugins.
• Christian Henden has some interesting plugins (mainly in the Public Domain), including 3D threshold methods: http://www.pvv.org/~perchrh/imagej/

Related projects

150px	The next generation ImageJ.
	The Konstanz kNowledge Information Mining Environment.
	µManager is an extensive software suite to interact with microscopes. It integrates nicely as an ImageJ plugin (Plugins>Micro-Manager>Micro-Manager Studio).
	OpenSPIM is an Open Access and Open Source project to make Single Plane Illumination Microscopy (SPIM) accessible to researchers working with, or on, SPIM technology.

Image Processing and Ethics

It becomes more and more important to have clear-cut guidelines what types of image processing are appropriate and what processing is questionable at best.

Here is a comprehensive list of 12 rules you need to follow if you want to perform science rather than art.

Input/Output

Movie support

There is a beta-quality Movie support for all of Fiji's supported platforms available via the update site http://fiji.sc/~schindelin/ffmpeg-plugins/ (see these instructions on how to follow an update site). It uses FFMPEG (which includes all the upstream changes of LibAV. As such, the plugin requires native, platform-dependent libraries that are shipped from the same update site.

Note that there is a similar project, based on javacv which seems to be superior to the FFMPEG plugins mentioned above.

Bio-Formats has started supporting parts of the Quicktime specification without relying on the native Quicktime4Java that is not even supported on 64-bit MacOSX, let alone Linux.

Image Processing

A pixel is not a little square. Really. It is not. Pixels may be spaced on a regular grid. But that does not make them square. Even thinking about them as squares will harm your analysis, since it is simply wrong.

Explore the Hypermedia Image Processing Reference of the Department of Artificial Intelligence in the University of Edinburgh for an extensive overview of available image processing techniques.

The University of Edinburgh also has the rather complete CVonline compendium of Computer Vision.

A scientific image is not a photograph!

External tutorials.

Programming in science

In research Software should be treated just like materials: if you publish your results, you should publish the software (including source code), too.

Even Nature says that your code is good enough; you should publish it if you want to be a good scientist.

If you're still unsure and think that your code is not good enough, then publish it under a license appropriate for science (CRAPL).

Java

• An introduction to Java for kids (ebook)
• Mixing light-weight (Swing) and heavy-weight (AWT) components

• A generics tutorial

• Infrequently Asked Questions about Java

• Effective Java

• Details about Sun's/Oracle's Java Just-In-Time (JIT) compiler, and in particular, performance techniques of the JIT.

Miscellaneous

• An explanation where ImageJ's icon's microscope comes from.

Imaging Networks and Facilities

• Imaging Facility Network (Dresden Biopolis)